In this thesis, we explore the adaptability of biological nanopores towards the detection of proteins and their modifications. First, beta-barrel nanopores are modified to increase the retention and discrimantion of proteogenic peptides. An acidic-aromatic sensing region allowed the capture and detection of a mixture of peptides in the nanopore at low pH. These acidic-aromatic nanopores are then used to detect protein glycosylation, peptide chirality and isobaric peptide modifications.